Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase
ABSTRACT N6-methyladenosine (m6A), a ubiquitous RNA modification, is installed by METTL3-METTL14 complex. The structure of the heterodimeric complex between the methyltransferase domains (MTDs) of METTL3 and METTL14 has been previously determined. However, the MTDs alone possess no enzymatic activit...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2018-03-01
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| Series: | Protein & Cell |
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| Online Access: | http://link.springer.com/article/10.1007/s13238-018-0518-7 |
| _version_ | 1827851567459467264 |
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| author | Jinbo Huang Xu Dong Zhou Gong Ling-Yun Qin Shuai Yang Yue-Ling Zhu Xiang Wang Delin Zhang Tingting Zou Ping Yin Chun Tang |
| author_facet | Jinbo Huang Xu Dong Zhou Gong Ling-Yun Qin Shuai Yang Yue-Ling Zhu Xiang Wang Delin Zhang Tingting Zou Ping Yin Chun Tang |
| author_sort | Jinbo Huang |
| collection | DOAJ |
| description | ABSTRACT N6-methyladenosine (m6A), a ubiquitous RNA modification, is installed by METTL3-METTL14 complex. The structure of the heterodimeric complex between the methyltransferase domains (MTDs) of METTL3 and METTL14 has been previously determined. However, the MTDs alone possess no enzymatic activity. Here we present the solution structure for the zinc finger domain (ZFD) of METTL3, the inclusion of which fulfills the methyltransferase activity of METTL3-METTL14. We show that the ZFD specifically binds to an RNA containing 5′-GGACU-3′ consensus sequence, but does not to one without. The ZFD thus serves as the target recognition domain, a structural feature previously shown for DNA methyltransferases, and cooperates with the MTDs of METTL3-METTL14 for catalysis. However, the interaction between the ZFD and the specific RNA is extremely weak, with the binding affinity at several hundred micromolar under physiological conditions. The ZFD contains two CCCH-type zinc fingers connected by an anti-parallel β-sheet. Mutational analysis and NMR titrations have mapped the functional interface to a contiguous surface. As a division of labor, the RNA-binding interface comprises basic residues from zinc finger 1 and hydrophobic residues from β-sheet and zinc finger 2. Further we show that the linker between the ZFD and MTD of METTL3 is flexible but partially folded, which may permit the cooperation between the two domains during catalysis. Together, the structural characterization of METTL3 ZFD paves the way to elucidate the atomic details of the entire process of RNA m6A modification. |
| first_indexed | 2024-03-12T10:34:58Z |
| format | Article |
| id | doaj.art-cbbaef1486a4452ea26e0b63b79431b5 |
| institution | Directory Open Access Journal |
| issn | 1674-800X 1674-8018 |
| language | English |
| last_indexed | 2024-03-12T10:34:58Z |
| publishDate | 2018-03-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Protein & Cell |
| spelling | doaj.art-cbbaef1486a4452ea26e0b63b79431b52023-09-02T08:50:55ZengOxford University PressProtein & Cell1674-800X1674-80182018-03-0110427228410.1007/s13238-018-0518-7Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferaseJinbo Huang0Xu Dong1Zhou Gong2Ling-Yun Qin3Shuai Yang4Yue-Ling Zhu5Xiang Wang6Delin Zhang7Tingting Zou8Ping Yin9Chun Tang10National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural UniversityCAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of SciencesCAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of SciencesCAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of SciencesCAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of SciencesCAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of SciencesNational Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural UniversityCAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of SciencesABSTRACT N6-methyladenosine (m6A), a ubiquitous RNA modification, is installed by METTL3-METTL14 complex. The structure of the heterodimeric complex between the methyltransferase domains (MTDs) of METTL3 and METTL14 has been previously determined. However, the MTDs alone possess no enzymatic activity. Here we present the solution structure for the zinc finger domain (ZFD) of METTL3, the inclusion of which fulfills the methyltransferase activity of METTL3-METTL14. We show that the ZFD specifically binds to an RNA containing 5′-GGACU-3′ consensus sequence, but does not to one without. The ZFD thus serves as the target recognition domain, a structural feature previously shown for DNA methyltransferases, and cooperates with the MTDs of METTL3-METTL14 for catalysis. However, the interaction between the ZFD and the specific RNA is extremely weak, with the binding affinity at several hundred micromolar under physiological conditions. The ZFD contains two CCCH-type zinc fingers connected by an anti-parallel β-sheet. Mutational analysis and NMR titrations have mapped the functional interface to a contiguous surface. As a division of labor, the RNA-binding interface comprises basic residues from zinc finger 1 and hydrophobic residues from β-sheet and zinc finger 2. Further we show that the linker between the ZFD and MTD of METTL3 is flexible but partially folded, which may permit the cooperation between the two domains during catalysis. Together, the structural characterization of METTL3 ZFD paves the way to elucidate the atomic details of the entire process of RNA m6A modification.http://link.springer.com/article/10.1007/s13238-018-0518-7RNA modificationN6-methyladenosineMETTL3target recognition domainzinc fingerparamagnetic relaxation enhancement |
| spellingShingle | Jinbo Huang Xu Dong Zhou Gong Ling-Yun Qin Shuai Yang Yue-Ling Zhu Xiang Wang Delin Zhang Tingting Zou Ping Yin Chun Tang Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase Protein & Cell RNA modification N6-methyladenosine METTL3 target recognition domain zinc finger paramagnetic relaxation enhancement |
| title | Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase |
| title_full | Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase |
| title_fullStr | Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase |
| title_full_unstemmed | Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase |
| title_short | Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase |
| title_sort | solution structure of the rna recognition domain of mettl3 mettl14 n6 methyladenosine methyltransferase |
| topic | RNA modification N6-methyladenosine METTL3 target recognition domain zinc finger paramagnetic relaxation enhancement |
| url | http://link.springer.com/article/10.1007/s13238-018-0518-7 |
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